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illumina beadarray expresion matrix transformation problem

This is my first time dealing with beadarray data. For Affymetrix microarray data, I can easily log-transform it. However for beadarray data, after log-transformation, the shape of the data didn't change too much.

For one single sample,

After log transformation:

plot

So how can I transform the data into normal shape?

microarray gene-expression bead-array r
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updated by Ram Ram • written by lovetl2002 • lovetl2002

Did you normalize before log transformation ? like quantile or spline (RSN) ?

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written by poisonAlien poisonAlien

2 answers

Have you looked at the lumiT() and lumiN() functions in the lumi package?

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written by andrew.j.skelton73 andrew.j.skelton73

I would highly recommend reading through the manual for beadarray package

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written by Ying W Ying W

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